Introduction

Most of my work is in Torres Strait in collaboration with Traditional Owners, with a focus on stock assessment and harvest strategies for their hand collectable fisheries. I have spent a lot of time underwater collecting data and am now more involved on the other “dark” side, with analyses and data outputs. I never used code before data school.

My Project

The Torres Strait ’Beche-de-mer (sea cucumber) Fishery (TSBDM) has become an important source of income for Torres Strait islanders since the early 1990s. While most beche-de-mer species stocks are in good numbers, several species are closed to fishing, or recovering from fishing pressure such as Sandfish, Black teatfish and Surf redfish. This has led to increased fishing pressure on other species, including the Prickly redfish and Curryfish.

Fishery dependent data (logbooks) were introduced to the TSBDMF in December 2017. However, there is considerable uncertainty about the status of many beche-de-mer populations. A stock survey is at present, still the only way to find out the status of fished beche-de-mer populations in Torres Strait. Previous stock surveys have been undertaken in 1995, 2002, 2005 and 2009. The most recent survey was undertaken in 2019/20.

Thank you to Torres Strait Islander fishery representatives, and to all Torres Strait Islanders for regularly hosting us on their land and supporting this research.

My goals

Data exists for the TSBDMF from field surveys undertaken in 1995, 2002, 2005, 2009 and now 2019/20. Previously excel has been used for anlayses for stratitfied mean comparisons and stock estimates of species abundance. My goal is to work up the 2019/20 data set and build on previous analyses using R for fishery statistics of CPUE, as well as modelling to look at stock trends.

Stock survey

SCUBA divers surveyed transects for sea cucumbers species in November 2019 and January 2020. Sea cucumbers were recorded and processed, along with a number of environmental indicators and habitat measurement (Table1).

Table 1: Field data

holothuria_whitmaei	zone	samocc	strata	count_site_id	area_hectare	longitude	latitude	depth_finish
6.4523810	Barrier	2002	Reef edge	25	4263.384	144.0456	-10.186410	17.7600000
0.0000000	Barrier	2002	Reef top	2	2599.626	143.9492	-10.411155	2.5000000
8.9285714	Barrier	2002	Reef top buffer (200 m)	14	9341.058	143.9927	-10.300327	0.0000000
0.2604167	Cumberland	2002	Reef edge	48	4679.308	143.7410	-9.996976	17.5729167
2.3148148	Cumberland	2002	Reef top	54	30938.752	143.6748	-10.032286	0.3148148

Selfie with a White teatfish, Holothuria fuscogilva

Plots from R

Initial data anlayses for some high and medium value commercial species looked at length frequency profiles (Figure1) as well as average density estimates across survey years (Figure2).

Figure 1: Length frequency distribution for Black teatfish Holothuria whitmaei, over survey years.

When less is definitely more, but it was cool to see what outputs can be produced.

Figure 2: A = White teatfish, Holothuria fuscogilva B = Black teatfish, H. whitmaei C = Curryfish, Stichopus herrmanni D = Prickly redfish, Thelenota ananas

My Digital Toolbox

• R - dplyr, ggplot, ggpubr

My time went …

It was a rollercoaster! I appreciate the fact that you can type anything into google and guaranteed someone has already aksed the question and there are answers, especially stack overflow. The R community are altruistic.

Next steps

I plant to use ggplot to plot Catch Per Unit Effort data and will look at writing functions to capture other analyses currently run in Excel. I will also be trying modelr for looking at stock trends for species.

My Data School Experience

In addition to building on outputs from data school for my current sea cucumber project, I have already used R for real on other project work. A figure for a report needed updating with recent data, however the scientist that produced the plot previously has now retired. I was able to write the script needed and produced the exact plot, this has now been included in the technical report for a project milestone.

Do it! One day it just clicks and it’s kind of awesome, so don’t give up.

Acknowlegement Thanks to Stephen Pearce, Kerensa McElroy and Kristian Goodacre - as well as all the guest teachers and tutuors!